Autosomal linkage homologies, which are defined as the conserved linkage of pairs of homologous genes in different species, will be used to study the organization and evolution of the eukaryotic genome. Gene mapping will be used to provide more complete linkage maps of several eukaryotes. Species to be studied include house mice (Mus musculus) and the proto-chordate Botryllus schlosseri. Genes to be mapped include enzyme-encoding loci, endogenous retrovirus-like DNA sequences, and several biologically and medically important genes for which molecular probes have recently become available. In addition, an analysis of linkage homologies will be used to determine whether the fusibility and fertilization gene(s) in B. schlosseri represent a proto-major histocompatibility complex. Theoretical studies will be used to evaluate the null hypothesis that the arrangement of genes in the genome has no regulatory or functional significance and consequently that the only phenotypic effect of chromosomal rearrangements is reduced fertility in rearrangement heterozygotes. These studies include characterizing the functional relations between genes in conserved chrosomal segments, calculating the probabilities of linkage conservation, deriving the frequency distribution for lengths of conserved segments, comparing both the expected and empirical probabilities of conservation and the expected and empirical distribution of lengths of conserved segments, and using the lengths of conserved segments to calculate rates of chromosomal evolution. These studies will contribute to an understanding of the regulation and interaction of genes, and the effects of chromosomal rearrangements on gene expression and development.